A Manhattan Catholic priest was awaiting arraignment last night on charges of sexually abusing a 16-year-old altar boy in the rectory of their church, police said.

Jorge Pintado, 39, has been charged with sexual abuse after he allegedly groped the teen Tuesday evening in the rectory of the Good Shepherd Church in Inwood, just moments after he celebrated Mass, police said.

The victim, who also sings in the church choir, told cops that Pintado, an Ecuadorian immigrant, grabbed his genitals through his pants when he “hugged him,” sources said.

The teen also said Pintado had been hugging him “inappropriately” since June.

Under questioning, Pintado, who was arrested Wednesday morning, admitted his guilt in a videotaped statement, and also signed a confession, sources said.

Pintado, who moved to the city in 1990, has been celebrating Mass in Spanish once a week at the church for the past few years, said Good Shepherd’s head pastor, the Rev. Marcos Zamora.

He wasn’t authorized to work in the Archdiocese of New York, said spokesman Joe Zwilling. His last formal tie to the archdiocese ended in October 2000, when he left a Bronx parish for health and other reasons, Zwilling said.

“There’s nothing in the files to indicate any activity of this sort,” he said of the sex-abuse allegations against Pintado.

Pintado has also been charged with endangering the welfare of a child. If convicted of the charges, he faces up to a year behind bars.